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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2v7tSAH5'-fluoro-5'-deoxy-adenosine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2v7tSAH5'-fluoro-5'-deoxy-adenosine synthase/1.000
2v7uSAM5'-fluoro-5'-deoxy-adenosine synthase/0.785
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.498
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.493
1zgbA1EAcetylcholinesterase3.1.1.70.488
4araC56Acetylcholinesterase3.1.1.70.487
5d6lCAUBeta-2 adrenergic receptor/0.484
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.481
2rh1CAUBeta-2 adrenergic receptor/0.481
1dx6GNTAcetylcholinesterase3.1.1.70.479
2bpoFADNADPH--cytochrome P450 reductase/0.479
2zbvADNUncharacterized protein/0.479
3pm1ETHTH-type transcriptional regulator QacR/0.478
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.476
2pbzATPUncharacterized protein/0.475
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.473
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.473
3p0fBAUUridine phosphorylase 22.4.2.30.473
3fhxPLPPyridoxal kinase2.7.1.350.472
4b63NAPL-ornithine N(5)-monooxygenase/0.472
1vftDCSAlanine racemase/0.471
1ygkRRCPyridoxal kinase2.7.1.350.471
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.471
4rv9SAHD-mycarose 3-C-methyltransferase/0.471
1odcA8BAcetylcholinesterase3.1.1.70.468
2aouCQAHistamine N-methyltransferase2.1.1.80.468
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.467
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.467
4b68NAPL-ornithine N(5)-monooxygenase/0.467
2j3qTFLAcetylcholinesterase3.1.1.70.466
2ok8FADFerredoxin--NADP reductase, apicoplast/0.466
4m9aFDAAcyl-CoA dehydrogenase/0.466
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.465
4u140HKMuscarinic acetylcholine receptor M3/0.465
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.464
4azwSAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.464
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.464
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.463
2ed3SAHDiphthine synthase/0.463
3ou2SAHSAM-dependent methyltransferase/0.463
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.463
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.463
2ct8MSPMethionine--tRNA ligase6.1.1.100.462
4gdpFADPolyamine oxidase FMS1/0.462
1gpnHUBAcetylcholinesterase3.1.1.70.461
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.461
1q84TZ4Acetylcholinesterase3.1.1.70.460
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.459
3b3fSAHHistone-arginine methyltransferase CARM1/0.459
4e32DWNMethyltransferase/0.459
1vgqCAOFormyl-CoA:oxalate CoA-transferase/0.458
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.457
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.457
2cekN8TAcetylcholinesterase3.1.1.70.457
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.457
3ihgVAKAklavinone 12-hydroxylase RdmE/0.457
4b64NAPL-ornithine N(5)-monooxygenase/0.457
4b6uM7GEukaryotic translation initiation factor 4E type 3/0.457
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.457
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4gr9372Ribosyldihydronicotinamide dehydrogenase [quinone]/0.457
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.457
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.457
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.456
1votHUPAcetylcholinesterase3.1.1.70.456
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.456
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.456
4bfuZVUPantothenate kinase2.7.1.330.456
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.456
1ay0TPPTransketolase 12.2.1.10.455
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
1tllFMNNitric oxide synthase, brain1.14.13.390.455
1xmmM7Gm7GpppX diphosphatase3.6.1.590.455
2xukTZ5Acetylcholinesterase3.1.1.70.455
3ske054Genome polyprotein2.7.7.480.455
3v0p4GWHisto-blood group ABO system transferase/0.455
4b4vL34Bifunctional protein FolD/0.455
4jeyPLPAcetylornithine/succinyldiaminopimelate aminotransferase2.6.1.110.455
5c1gGDUHisto-blood group ABO system transferase/0.455
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.454
2w6cBM4Acetylcholinesterase3.1.1.70.454
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.453
2r0pK2CPutative FAD-monooxygenase/0.453
2xuhTZ4Acetylcholinesterase3.1.1.70.453
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3qfcFADNADPH--cytochrome P450 reductase/0.453
3sfy3FYUncharacterized protein/0.453
4jlm1NNDeoxycytidine kinase2.7.1.740.453
1xi2CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.452
2a3bCFFEndochitinase B13.2.1.140.452
2xlpNAPPutative flavin-containing monooxygenase/0.452
3c1oNAPEugenol synthase/0.452
3e23SAMUncharacterized protein/0.452
4bupSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.452
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.451
1qtiGNTAcetylcholinesterase3.1.1.70.451
1sg0STLRibosyldihydronicotinamide dehydrogenase [quinone]/0.451
1ta6177Prothrombin3.4.21.50.451
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.451
2y1w849Histone-arginine methyltransferase CARM1/0.451
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.451
3d4bDZDNAD-dependent protein deacetylase/0.451
3h3qH13Collagen type IV alpha-3-binding protein/0.451
3uyk0CXProbable NDP-rhamnosyltransferase/0.451
4bb2STRCorticosteroid-binding globulin/0.451
4oex5EOcGMP-specific 3',5'-cyclic phosphodiesterase/0.451
1thnADPAnti-sigma F factor/0.450
2pswCOAN-alpha-acetyltransferase 50/0.450
2xupTZ5Acetylcholinesterase3.1.1.70.450
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.450
3r8hZOMAldo-keto reductase family 1 member C3/0.450
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.450
4wljIK2Kynurenine--oxoglutarate transaminase 12.6.1.70.450
1obnASVIsopenicillin N synthase1.21.3.10.449
1x1j46DXanthan lyase/0.449
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.449
2pncCLUPrimary amine oxidase, liver isozyme/0.449
3h3sH15Collagen type IV alpha-3-binding protein/0.449
3imgBZ3Pantothenate synthetase6.3.2.10.449
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.449
4o6fSAHN-lysine methyltransferase SMYD2/0.449
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
1ve3SAMUncharacterized protein/0.448
1x1cSAHC-20 methyltransferase/0.448
2wzySQXSoluble acetylcholine receptor/0.448
2z78H86Geranylgeranyl pyrophosphate synthase/0.448
3bbpGTPRas-related protein Rab-6A/0.448
3nxyD2HDihydrofolate reductase1.5.1.30.448
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.448
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.448
4n9qFMNFMN-dependent NADH-azoreductase 1/0.448
1x8b824Wee1-like protein kinase2.7.10.20.447
2ejzSAHDiphthine synthase/0.447
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.447
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.447
3bk2U5PRibonuclease J/0.447
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1lnmDTXBilin-binding protein/0.446
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
1yhnGTPRas-related protein Rab-7a/0.446
2aj4ANPGalactokinase2.7.1.60.446
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.446
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.446
3ie3N11Glutathione S-transferase P2.5.1.180.446
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.446
3ndjJHZMethyltransferase/0.446
3ou6SAMSAM-dependent methyltransferase/0.446
3qftFADNADPH--cytochrome P450 reductase/0.446
3w5uFADFerredoxin/0.446
4b2gV1NUncharacterized protein/0.446
4b66NAPL-ornithine N(5)-monooxygenase/0.446
4bfwZVWPantothenate kinase2.7.1.330.446
4jzr4JREgl nine homolog 1/0.446
4mk928RGenome polyprotein2.7.7.480.446
1vfsDCSAlanine racemase/0.445
1w4lGL8Acetylcholinesterase3.1.1.70.445
1x1bSAHC-20 methyltransferase/0.445
2e94364Geranylgeranyl pyrophosphate synthase/0.445
2gmuPDGPutative pyridoxamine 5-phosphate-dependent dehydrase/0.445
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.445
3e6eDCSAlanine racemase/0.445
3pdnSFGHistone-lysine N-methyltransferase SMYD32.1.1.430.445
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
1dgfNDPCatalase1.11.1.60.444
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.444
2ha6SCKAcetylcholinesterase3.1.1.70.444
2vqbNAPPutative flavin-containing monooxygenase/0.444
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3h0vM2TS-adenosylmethionine decarboxylase proenzyme4.1.1.500.444
3ivcFG4Pantothenate synthetase6.3.2.10.444
3nhjA2ZRibosyldihydronicotinamide dehydrogenase [quinone]/0.444
3oy0OY0Carbonic anhydrase 24.2.1.10.444
3pqbVGPPutative oxidoreductase/0.444
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.444
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.444
4iix1EGMicrocin C7 self-immunity protein MccF/0.444
5a4vQUEGlutathione S-transferase F22.5.1.180.444
1u65CP0Acetylcholinesterase3.1.1.70.443
1w6rGNTAcetylcholinesterase3.1.1.70.443
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.443
2oatPFMOrnithine aminotransferase, mitochondrial2.6.1.130.443
2owgSAHDiphthine synthase/0.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3d2mCOAAmino-acid acetyltransferase/0.443
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3px3T3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.443
3uxhUXHRibosyldihydronicotinamide dehydrogenase [quinone]/0.443
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.443
4kxjP34Nucleoprotein/0.443
4l0t1V0Tankyrase-22.4.2.300.443
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.443
1lkeDOGBilin-binding protein/0.442
1ut6A8NAcetylcholinesterase3.1.1.70.442
2ckmAA7Acetylcholinesterase3.1.1.70.442
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.442
3arpDEQChitinase A/0.442
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
5czySAMEukaryotic huntingtin interacting protein B/0.442
1njjORXOrnithine decarboxylase/0.441
2gywOBIAcetylcholinesterase3.1.1.70.441
2z4zSC0Geranylgeranyl pyrophosphate synthase/0.441
3arvSAUChitinase A/0.441
3br3ETHTH-type transcriptional regulator QacR/0.441
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3f90FMNFlavodoxin/0.441
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.441
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.441
4a86H35Major pollen allergen Bet v 1-A/0.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
1cjkFOKAdenylate cyclase type 2/0.440
1cjkFOKAdenylate cyclase type 5/0.440
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1ry0PG2Aldo-keto reductase family 1 member C3/0.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.440
3lzzGDPUncharacterized protein/0.440
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.440
4dlcUMPDeoxyuridine triphosphatase, putative/0.440
5dsg0HKMuscarinic acetylcholine receptor M4/0.440